I have the same issue, I thought it was just a bug affecting me. I used to have the same issue about 3/4 years ago when I played a restarted Federation.
Its a shame that all the servers go down all at once, surelly Cryptic doesn't have all the servers in one place? If they dont and have say 3 groups of servers ie.. US, Europe and Far East I cant understand why they cant bring it down one at a time during night hours?